// To be run from pce/casp5/t0134

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time



OutFilePrefix decoys/

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0134.rand
Time



InFilePrefix 
ReadTemplateAtoms Template.atoms

Time

ReadFragmentAlignment 1kyfA/T0134-1kyfA-heavy-str-local.pw.a2m
ReadFragmentAlignment 1b9kA/T0134-1b9kA-heavy-str-local.pw.a2m
ReadFragmentAlignment 1qtsA/T0134-1qtsA-heavy-str-local.pw.a2m
ReadFragmentAlignment 1e42A/T0134-1e42A-heavy-str-local.pw.a2m


// ReadConformPDB decoys/T0134.try7-opt-scwrl.pdb
// NameConform T0134.try8-try7
// ReadConformPDB decoys/T0134.try6-opt-scwrl.pdb
// NameConform T0134.try8-try6
// ReadConformPDB decoys/T0134.try5-opt-scwrl.pdb
// NameConform T0134.try8-try5
// ReadConformPDB decoys/T0134.try4-opt.pdb
// NameConform T0134.try8-try4
// ReadConformPDB decoys/T0134.try3-opt.pdb
// NameConform T0134.try8-try3
// ReadConformPDB decoys/T0134-try2-opt.pdb
// NameConform T0134.try8-try2
// 

ReportCost undertaker-try11.rdb

 TryAllAlign shrink 0.4 min_keep_length 5 
 TryAllAlign shrink 0.4 min_keep_length 5 cumulative
NameConform T0134.try11-al2
PrintConformPDB T0134.try11-al2.pdb edges

TryAllAlign shrink 0. min_keep_length 1 
TryAllAlign shrink 0. min_keep_length 1 cumulative
NameConform T0134.try11-al4
PrintConformPDB T0134.try11-al4.pdb edges

 TryAllAlign shrink 0.3 min_keep_length 4 
 TryAllAlign shrink 0.3 min_keep_length 4 cumulative
NameConform T0134.try11-al6
PrintConformPDB T0134.try11-al6.pdb edges

TryAllAlign shrink 0.1 min_keep_length 2 
TryAllAlign shrink 0.1 min_keep_length 2 cumulative
 NameConform T0134.try11-al8
 PrintConformPDB T0134.try11-al8.pdb edges

TryAllAlign shrink 0.2 min_keep_length 3
TryAllAlign shrink 0.2 min_keep_length 3 cumulative
 NameConform T0134.try11-al10
 PrintConformPDB T0134.try11-al10.pdb edges

 TryAllAlign shrink 0. min_keep_length 1 
 TryAllAlign shrink 0. min_keep_length 1 cumulative
 NameConform T0134.try11-al12
 PrintConformPDB T0134.try11-al12.pdb edges

CostConform
Time



// The following alignments are not as good as the ones tried above,
// so are not used in getting the starting point.

InFilePrefix 
ReadFragmentAlignment T0134.t2k.frag

Include T0134.undertaker-align.script 

InFilePrefix 
ReadFragmentAlignment T0134.t2k-2track-undertaker.a2m



InFilePrefix 1kyfA/
    include read-alignments.under
InFilePrefix 1b9kA/
    include read-alignments.under
InFilePrefix 1qtsA/
    include read-alignments.under
InFilePrefix 1e42A/
    include read-alignments.under
InFilePrefix 

OutFilePrefix
PrinttemplateAtoms Template.atoms
OutFilePrefix decoys/


Time



InitMethodProbs InsertAlignment 0 \
	ClashingRotamer 0.5 \
	InsertFragment 3 \
	CrossOver 0 \
	CrossAndInsert 2 \
	TwoFragment 1 \
	InsertSpecificFragment 5 \
	ReduceBreak 7 \
	CloseGap 0.1 \
	OptSubtree 0.03 \
	JiggleSubtree 0.03 \
	ReduceClash 1 \
	InsertSSBond 0

NameConform T0134.try11
OptConform pool_size 70 num_gen 60 gen_size 150 super_iter 20 pdb \
	use_all scwrl_each
NameConform T0134.try11-opt
PrintConformPDB T0134.try11-opt.pdb edges

SCWRLConform
NameConform T0134.try11-opt-scwrl
PrintConformPDB T0134.try11-opt-scwrl.pdb

CostConform
Time

quit